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Release 1.7.12 contains solutions for providing an easier install solution of i2b2, redesigned Find Terms, totalnum counting scripts, new Authentication protocols, and REDCAP import. Also included are are other enhancements to the i2b2 Webclient, the ACT ontology, and bug fixes.
After reading this documentation, please go to the Upgrade Notes page the Quick Upgrade Guide for the details about upgrading your i2b2 software. If you are installing from scratch, additionally refer to the refer instead to the Quick Install Guide (and optionally the full i2b2 Installation Guide on the i2b2 Community Wiki. The install guide will take you through the entire installation process.
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i2b2 Release 1.7.12
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i2b2
Release
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Release Date: November 21 December, 2019
Table of Contents |
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Highlight of Features
Backend Features
- Easier Install
- One step WARPre-file build and optional prebuilt WAR filebuilt War file for easier distributions of the application
- Properties files are moved from static files to a table in the database
- Authentication protocol support for OKTA , NTLM v2 Need some documentation on this...and NTLM v2.
- Database scripts to generate Totalnum counts for Ontology Terms for POSTGRESQL, ORACLE and SQL SERVER databases
- REDCap data import into i2b2, with ontology creation from REDCap forms
- Documentation updates for Apache Webserver timeout settings for previous queries run We still need to do this I think?run.
Frontend Features
Redesigned Find Terms By Name
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Community-Contributed Features
Contribution | Contributor | |
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ACT Technology and Data Harmonization Team University of Pittsburgh | ||
Easier-to-read counts | Nick Brown and Griffin Weber Beth Israel Deaconess Medical Center | |
Robert Bradford University of North Carolina | ||
Totalnum in find terms | Mauro Bucalo University of Pavia | |
Visual Design of new Find Terms | Leaf Team University of Washington | |
Totalnum Counter for Postgres | Dan Vianello Center for Biomedical Informatics, Washington University in St. Louis | (Part of overall totalnum scripts in this release.) |
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Easier i2b2 Install
The i2b2 server can now be installed in three or four steps:
- (Optional) Build the war from source. Run in the edu.harvard.i2b2.server-common folder:
ant clean dist war - Copy the i2b2.war from the dist folder (or the binary release zip file) to /opt/wildfly-VERSION-Final/standalone/deployments/ folder.
- Run the data build for all the cell (PM, HIVE, ONT and CRC) . In the Hive there is a new table called HIVE_CELL_PARAM which contains all the previous XML and properties file.
- Modify the *-ds.xml in the deployment folder to point to the database
using a pre-built war file instead of having to build it from source, or the war file can be built from source much more easily. More information is in the updated Installation Guide. The properties files are now stored in the database.
Anchor Authentication-protocol-support Authentication-protocol-support
Authentication Protocol Support for NTLM2/OKTA
User Set up with OKTA Configuration: On the Admin page, under Manage Users,
Add a Parameter domain and assign the values as below. Parameter value will be your institution domain name.
Add a second parameter domain_controller as below. Parameter value will be your institution domain_controller value
Add the final parameter authentication_method as below. Parameter value will be OKTA
User Set up with NTLM2 Configuration: On the Admin page, under Manage Users,
Add a Parameter domain and assign the values as below. Parameter value will be your institution domain name.
Add a second parameter domain_controller as below. Parameter value will be your institution domain_controller value
Add the final parameter authentication_method as below. Parameter value will be NTLM2
RedCap Import Setup Anchorredcap redcap
redcap | |
redcap |
TODO: We need some documentation on what features are supported and what aren't.
Currently, the following REDCAP Features are supported in i2b2.
- Project level :
- Only one unique redcap project id can be assigned to each i2b2 project( system finds the first project it encounters and assigns it, so two projects cannot have same REDCAP project id:
- Form level:
- Renaming a Form in Redcap will create a new record in table access instead of updating the original record which means in i2b2 the original survey will still show in Ontology in addition to creating the renamed survey as a new Ontology item.
- On adding a new Field/editing a field in the REDCAP form, the form needs to be explicitly associated with the record again to take effect in i2b2
- Data triggers happen only on Form SAVE button.
- Only Form SAVE as a URL survey or Admin edit/add record Saves, triggers i2b2 Ontology creation. Other forms of Form creation in REDCAP- by Data import tool, API format, will not trigger Ontology creation in i2b2)
- Ontology is only displayed in Tree structure format in i2b2. Pop up display (sometimes called query-by-value) is not supported. (example as below)
- There is no mapping of records submitted in REDCAP to existing patient_ids in i2b2. The scope of this release is limited to adding new record rows in Observation_fact table and Updating the fields of records added.
- Field level:
- The following project fields from REDCAP are supported in i2b2.
- TEXT BOX
- CHECKBOX
- RADIO BUTTON
- DROPDOWN
- YES-NO
- TRUE-FALSE
- SLIDER / VISUAL ANALOG SCALE
- DESCRIPTIVE TEXT
- NOTES BOX
- SIGNATURE
- DYNAMIC QUERY(SQL)
- Text box (Short text)Number and Date/Time ) with Validation capability in REDCAP - validation will work only as a simple text String search in i2b2
- Check box, Multiple Choice , Yes-No, True-False Form fields will appear as a Tree format in i2b2 ( Popup display is not supported)
- The following project fields from REDCAP are supported in i2b2.
REDCAP SETUP CONFIGURATION
1) Set Project Params (PM_PROJECT_PARAM)
Name | Value | Description |
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REDCP_TOKEN REDCAP_TOKEN_PID_{pid} | (7B42348B7C51123432048B51EAA) | Required:
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REDCAP_SURVEY_FORMPROJECT | (profilepid) | Required: This is the name of the Data Collection Instruments to associate this project with, in this example it is set to the 'Profile' Set the Value parameter to the pid value from the Redcap project url. |
REDCAP_ONTOLOGY_REFRESH | Y | Optional, Defaults to Y N - Do Not regenerate the metadata ontology. NOTE: When first setting up the i2b2/redcap this needs to be set to Y at least one once or the ontology will not be created. |
REDCAP_ROOT_ONTOLOGY | \REDCAP\ | Optional, Defaults to \REDCAP\ |
REDCAP_ONTOLOGY_FORMAT | tree | Optional, Defaults to tree tree - All enumerated values, Yes/No will be children on the ontology The only exception is items with checkbox, which will always be a popup |
RECAP_PROTECTED_ROLE | DATA_PROT | Optional, Defaults to DATA_PROT If this redcap form has the identified value set to true, than then this ontology will be protected and only users with the following i2b2 access role will be able to access it. |
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Click Test to verify connection
3) Give Editor role to the project for AGG_SERVICE_ACCOUNT( optional DATA_PROT, DEID, LDS)
4) Submit a form and check to see if the ontology was created.
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- In the Release_1-7/NewInstall/Metadata/ run the ant script to create the stored procedures.
- POSTGRESQL : ant -f data_build.xml db_metadata_run_total_count_postgresql
- ORACLE : ant -f data_build.xml db_metadata_run_total_count_oracle
- SQL SERVER : ant -f data_build.xml db_metadata_run_total_count_sqlserver
- Execute the RunTotalNum stored procedure on your database. This can take several hours.
Example Usage:
Oracle:
begin
RUNTOTALNUM('observation_fact','i2b2demodata');
end;
Note: If you get the error as: ERROR at line 1: ORA-01031: insufficient privilege, then run the command:
grant create table to (DB USER)
SQL server:
exec RUNTOTALNUM
PostgreSQL:
select RUNTOTALNUM('observation_fact','public')
-- (replace 'public' by the schema name for the fact table)
-- If using a schema other than public for metadata, you might need to run "set search_path to 'i2b2metadata','public' " first as well
3. When finished, verify it is complete by checking that c_totalnum columns in your ontology tables contain numbers (not nulls).
These total counts
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will be visible in the ontology browser in the web client.
ACT Ontology Setup
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This will allow you to install the ACT ontology as a separate project in i2b2. Note that this will create a project with ONLY the ontology - no data. At this time, using the demodata with the ACT ontology is not supported. You will need to load your own data to run queries using the ontology.
- In the Release_1-7/NewInstall/Metadata/db.properties file change the db.project from demo to
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- act
- Create new Project ACT in the Admin tool
- Add AGG SERVICE Account to the Project
- Add new dblookup-row with parameters under CRC, Ontology and workplace to set up the project path( example as in below)
- Run the ant script against create_metadata_tables_release_1-7 and db_metadata_load_data.
This will create the new ACT Ontology structure under project ACT.
Using Extended Query-By-Value Flags Anchorflags flags
flags | |
flags |
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- Small changes to the i2b2 Database.
- Property files were moved into the database in the new Hive table HIVE_CELL_PARAMS.
- Query type classname property moved from the properties file to the CRC table QT_QUERY_RESULT_TYPE in a new CLASSNAME field
- Totalnum counts to Ontology Terms in the demo data that is delivered with the software along with the Stored procedures used for creating the counts.
- ACT Ontology
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